Folders vanishing from our Windows 2003 file server

I have a Windows 2003 file server that is a member of our 2008r2 Active Directory domain. Many users scan to a folder on the C drive of this server and each user has their own sub folder under the scan folder. Today all subfolders that start with a letter past M in the alphabet vanished!!! I first went to see if I had them backed up, but in searching for an individual users folder I found them, even though they were not visible. I copied the folders to a different location on the C drive and they are now visible with all data inside. How could this have happened? Any clues on how I can troubleshoot this?

windows explorer by default does not show files with the System Attribute

i.e.
A C:\Users\David\DevelopmentStorageDb22.mdf
A C:\Users\David\DevelopmentStorageDb22_log.ldf
A SH I C:\Users\David\NTUSER.DAT
A SH C:\Users\David\ntuser.dat.LOG1
A SH C:\Users\David\ntuser.dat.LOG2

I guess I am not understanding or explaining this right. I do not know what file attributes has to do with this....Subfolders that have existed for years and users and scanned PDF documents to for years, just vanished today but when I log into the server directly and do a SEARCH ie "JIM DOCS" the folder appears and looks like it is in the proper path. I can copy and past the folder to another PC and recover the data, but if I go back and try to browse to the original folder it does not appear to be there. It is like they are hidden, but a generl search of the C drive finds them

Featured Post

Work with freelancers specializing in everything from database administration to programming, who have proven themselves as experts in their field. Hire the best, collaborate easily, pay securely, and get projects done right.